chap 8 - gene expression

- they have the same genome, but express different RNAs and proteins

- A typical cell expresses
~20% of its 25,000 genes
- A cell can change the expression of its genes in response to external signals

Eukaryotic gene expression can be controlled at many steps from DNA --> RNA --> Protein
- Transcriptional control is most common control point: DNA to RNA - ensure no unecessary intermediates synthesized

1. controlling when and how often a given gene is transcribed
2. Controlling how RNA transcript is spliced or otherwise processed
3. selecting which mRNAs are exported from the nucleus to the cytosol
4. regulating how quickly certain mRNA molecules are degraded
5. selecting which mRNA are translated into protein by ribsomes
6. regulating how rapidly specific proteins are destroyed after they have been made

processes that regulate protein concentration --
Rate of transcription: 73%
mRNA translation: 8%
Protein degration: 8%
mRNA degration: 11%
- the concentration of a protein is controlled

contain all of the genetic info to form a complete organism
- Cells can change the genes they express without altering the nt sequence of their DNA
ex. a nuclelus removed from a differentiated cell of an adult cow can be introduced to enucleated egg from a different cow to give rise to a calf. Different calves produced from the same differtiated cell donor are all clones of the donor and therefore GENETICALLY IDENTICAL -- a type of nuclear transportation
- the various cell types differ not bc of genes, but bc they express them differently

RNAP II + general transcription factors

-- which promoters assemble preinitiation complexes
-- rate at which RNAP initiates new rounds of transcription

identifying all mRNAs found in certain conditions
ex. Change in conditions during expt.
- Yeast grown in glucose deplete it as ethanol is made, they then use ethanol as a carbon source.
- Yeast at early stages will express genes for glucose utilization and later for ethanol utilization
(tuning on genes that are needed to deal with ethanol --
turn on and off genes to which enzymes need to deal with glucose (specific))

- Displays higher than average expression are red and lower than average are green
- Each class of tumors has its characteristic spectrum of expressed genes. In this case the unk type yellow tumor was judged to be a lung cancer because its pattern of gene expression was similar to those of a series of already- identified lung cancers.

- Transcription is controlled by proteins binding to regulatory DNA sequences
- gene expression begins at the promoter, where transcription is initiated.
- In selective gene transcription a “decision” is made about which genes to activate.
- DNA regulatory sequences are used to switch genes on/off
- Transcriptional regulators bind to these sequences
- In the most general sense, two types of regulatory proteins may bind DNA— repressor proteins and activator proteins.

- ACTIVATORS
Positive regulation —Gene is not normally transcribed; an activator protein binds to stimulate transcription.
- turning on a gene that is normally off
- enhancer region: activates bind to enhance the expression of the gene

- REPRESSORS
Negative regulation —Gene is normally transcribed, but binding of a repressor protein prevents transcription.
- silent - blocks RNA polymerase from blocking that area
-specific conditions

- Surface of protein fits tightly against special nt-specific surface features of the double helix in that region
- Usually binds to major helix with ionic, hydrogen and hydrophobic interactions without disrupting the base pair hydrogen bonds
- Only one contact is shown, but usually 10-20 base pair to protein contact is made
- A bond to a T - complementary hydrogen bonding; transition factors recognizes the amine because certain atoms bind to hydrogen bonding that interact from the transcription factor — could recognize and does not bind to the same area

- A SINGLE
- Coordinate expression of genes making enzymes in same pathway
- If trp conc. low, bacterium expresses enzymes needed to make trp; if trp abundant, these genes are repressed
Prokaryotes: have operons for making tripaphan (an amino acid) — in this case there are five genes and five enzymes that produces tripanphan so it could be used for protein synthesis — these enzymes all get turned on and turned off at the same time
they are put together on the same gene; 5 different proteins (all responding to the same operator - specific DNA sequence to turn on and off the same genes)
controlled by a single regulatory sequence called Trp Operator

- coordinate expression of 5 genes
- Level of tryptophan regulates the activity of the polymerase transcribing the tryptophan operon
- Inactive repressor is constitutively expressed

Lets suppose inside the cell there is very little Trp present (usually the case) — low amount inside the cell then inactive repressor protein will REMIAN inactive bc there is not enough Trp to actually bind onto the allosteric site of the inactive repressor protein to activate it — so gene is expressed to produce repressor mRNA and that mRNA is used to form inactive repressor protein, trp will not bind to the protein and will not activate it so nothing will bind to the operator section — nothing will block the transcription of these genes (the RNA polymerase will easily bind to the promoter section — and move along 5 structural genes — produces mRNA used by ribosomes — trp aa is formed) — bc its low needs more trp to function properly

When TRP rises (very high intracellular) — excess of the TRP molecules — some will act as a corepressor binding to the allosteric side of the inactive repressor protein and activates the protein by changing its 3D shape and the active form of this repressor protein will bind to the operator (green section of the operon) — inhibiting RNA polymerase from transcribing the 5 genes (not producing mRNA molecules — no synthesis) — the bacterial cell wants to conserve as much energy as possible no need to form trp when there is already too much

- all proteins same metabolic pathway

- occurs at a distance
- Looping of DNA allows contact between activator protein bound to enhancer and transcription complex bound to promoter
- Promotes or represses assembly of initiation complex
- 100 - 1000 nt apart

1. An activator protein bound to a distant enhancer attracts RNA polymerase and
the general transcription factors to the promoter.
2. Looping of the intervening DNA permits contact between the activator and the transcription initiation complex bound to the promoter.
3. In the case shown here, a large protein complex called Mediator serves as a go-between. The broken stretch of DNA signifies that the segment of DNA between the enhancer and the start of transcription varies in length, sometimes reaching tens of thousands of nucleotide pairs.
4. The TATA box is a DNA recognition sequence for the first general transcription factor that binds to the promoter (see Figure 7–12). Some eukaryotic activator proteins bind to DNA as dimers, but others bind DNA as monomers, as shown.

- affects the initiation of transcription by modulating chromatin structure
- Activator proteins can recruit histone modifying enzymes and chromatin-remodeling complexes to the promoter region

- Nucleosomes contain DNA and histones in a tight complex, inaccessible to RNA polymerase.
- Each histone has a positively charged “tail” at its N-terminus.
- Histone acetyltransferases change the tail’s charge by adding acetyl groups to the amino acids (less “+” so lower affinity for “-” charge on DNA.
- This opens up nucleosomes and activates transcription.
- Activators attract histone acetylases and repressors attract histone deacetylases

- can coordinate the expression of many different genes
- In eukaryotes, many genes involved in same pathway are on different chromosomes
- Series of genes with activator proteins bound; however, not efficient activation
- Additional transcription regulator (glucocorticoid receptor + hormone) binds to the regulatory sequence of these genes
- Now efficient expression of genes as a set
ex. Transcription factors for PEPCK gene

phosphopenolpyruvate carboxykinase catalyzes a rate-controlling step in gluconeogensis
- gene needed to make gluclose
- there could be many reasons why genes are turned on and off

- Eukaryotic gene expression can be regulated in the nucleus before/after mRNA export
- Control mechanisms include alternative splicing of pre-mRNA, microRNAs, translation repressors, or regulation of protein breakdown.

- Protein and mRNA concentrations are not consistently related—governed by factors acting after mRNA is made.
- Cells can block mRNA translation or alter how long new proteins persist in the cell.
Multiple ways to regulate mRNA translation:
- miRNAs can inhibit translation
- GTP cap on 5′ end of mRNA can be modified—if cap is modified mRNA is not translated
- Repressor proteins can block translation directly